keyword
MENU ▼
Read by QxMD icon Read
search

chromatin conformation

keyword
https://www.readbyqxmd.com/read/29145649/single-molecule-compaction-of-megabase-long-chromatin-molecules-by-multivalent-cations
#1
Anatoly Zinchenko, Nikolay V Berezhnoy, Sai Wang, William M Rosencrans, Nikolay Korolev, Johan R C van der Maarel, Lars Nordenskiöld
To gain insight into the conformational properties and compaction of megabase-long chromatin molecules, we reconstituted chromatin from T4 phage DNA (165 kb) and recombinant human histone octamers (HO). The unimolecular compaction, induced by divalent Mg2+ or tetravalent spermine4+ cations, studied by single-molecule fluorescence microscopy (FM) and dynamic light scattering (DLS) techniques, resulted in the formation of 250-400 nm chromatin condensates. The compaction on this scale of DNA size is comparable to that of chromatin topologically associated domains (TAD) in vivo...
November 14, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29137603/clustertad-an-unsupervised-machine-learning-approach-to-detecting-topologically-associated-domains-of-chromosomes-from-hi-c-data
#2
Oluwatosin Oluwadare, Jianlin Cheng
BACKGROUND: With the development of chromosomal conformation capturing techniques, particularly, the Hi-C technique, the study of the spatial conformation of a genome is becoming an important topic in bioinformatics and computational biology. The Hi-C technique can generate genome-wide chromosomal interaction (contact) data, which can be used to investigate the higher-level organization of chromosomes, such as Topologically Associated Domains (TAD), i.e., locally packed chromosome regions bounded together by intra chromosomal contacts...
November 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29128709/integrating-experiment-theory-and-simulation-to-determine-the-structure-and-dynamics-of-mammalian-chromosomes
#3
REVIEW
G Tiana, L Giorgetti
Eukaryotic chromosomes are complex polymers, which largely exceed in size most biomolecules that are usually modelled in computational studies and whose molecular interactions are to a large extent unknown. Since the folding of the chromatin fiber in the cell nucleus is tightly linked to biological function and gene expression in particular, characterizing the conformational and dynamical properties of chromosomes has become crucial in order to better understand how genes are regulated. In parallel with the development of experimental techniques allowing to measure physical contacts within chromosomes inside the cell nucleus, a large variety of physical models to study the structure and mechanisms of chromosome folding have recently emerged...
November 8, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/29113562/utilizing-networks-for-differential-analysis-of-chromatin-interactions
#4
Lu Liu, Jianhua Ruan
Chromatin conformation capture with high-throughput sequencing (Hi-C) is a powerful technique to detect genome-wide chromatin interactions. In this paper, we introduce two novel approaches to detect differentially interacting genomic regions between two Hi-C experiments using a network model. To make input data from multiple experiments comparable, we propose a normalization strategy guided by network topological properties. We then devise two measurements, using local and global connectivity information from the chromatin interaction networks, respectively, to assess the interaction differences between two experiments...
October 19, 2017: Journal of Bioinformatics and Computational Biology
https://www.readbyqxmd.com/read/29106613/3div-a-3d-genome-interaction-viewer-and-database
#5
Dongchan Yang, Insu Jang, Jinhyuk Choi, Min-Seo Kim, Andrew J Lee, Hyunwoong Kim, Junghyun Eom, Dongsup Kim, Inkyung Jung, Byungwook Lee
Three-dimensional (3D) chromatin structure is an emerging paradigm for understanding gene regulation mechanisms. Hi-C (high-throughput chromatin conformation capture), a method to detect long-range chromatin interactions, allows extensive genome-wide investigation of 3D chromatin structure. However, broad application of Hi-C data have been hindered by the level of complexity in processing Hi-C data and the large size of raw sequencing data. In order to overcome these limitations, we constructed a database named 3DIV (a 3D-genome Interaction Viewer and database) that provides a list of long-range chromatin interaction partners for the queried locus with genomic and epigenomic annotations...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29098627/exercise-training-and-epigenetic-regulation-multilevel-modification-and-regulation-of-gene-expression
#6
Ursula Paula Renó Soci, Stephano Freitas Soares Melo, João Lucas Penteado Gomes, André Casanova Silveira, Clara Nóbrega, Edilamar Menezes de Oliveira
Exercise training elicits acute and adaptive long term changes in human physiology that mediate the improvement of performance and health state. The responses are integrative and orchestrated by several mechanisms, as gene expression. Gene expression is essential to construct the adaptation of the biological system to exercise training, since there are molecular processes mediating oxidative and non-oxidative metabolism, angiogenesis, cardiac and skeletal myofiber hypertrophy, and other processes that leads to a greater physiological status...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29098179/dna-topology-in-chromatin-is-defined-by-nucleosome-spacing
#7
Tatiana Nikitina, Davood Norouzi, Sergei A Grigoryev, Victor B Zhurkin
In eukaryotic nucleosomes, DNA makes ~1.7 superhelical turns around histone octamer. However, there is a long-standing discrepancy between the nucleosome core structure determined by x-ray crystallography and measurements of DNA topology in circular minichromosomes, indicating that there is only ~1.0 superhelical turn per nucleosome. Although several theoretical assumptions were put forward to explain this paradox by conformational variability of the nucleosome linker, none was tested experimentally. We analyzed topological properties of DNA in circular nucleosome arrays with precisely positioned nucleosomes...
October 2017: Science Advances
https://www.readbyqxmd.com/read/29095607/how-does-the-proliferating-cell-nuclear-antigen-modulate-binding-specificity-to-multiple-partner-proteins
#8
Hubert Li, Manbir Sandhu, Linda H Malkas, Robert J Hickey, Nagarajan Vaidehi
Proliferating cell nuclear antigen (PCNA) is a member of the family of sliding clamp proteins that serves as a clamp during DNA repair, DNA replication, cell cycle control, and multiple forms of chromatin modification. PCNA functions as a homotrimer and complexes with multiple proteins in order to carry out each of these varied functions. PCNA binds to different partner proteins in the same region of its structure, called the " interdomain connecting loop", but with different affinities. This interdomain connecting loop is an intrinsically disordered region that takes different conformations when binding to different partner proteins...
November 17, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/29094699/two-independent-modes-of-chromatin-organization-revealed-by-cohesin-removal
#9
Wibke Schwarzer, Nezar Abdennur, Anton Goloborodko, Aleksandra Pekowska, Geoffrey Fudenberg, Yann Loe-Mie, Nuno A Fonseca, Wolfgang Huber, Christian H Haering, Leonid Mirny, Francois Spitz
Imaging and chromosome conformation capture studies have revealed several layers of chromosome organization, including segregation into megabase-sized active and inactive compartments, and partitioning into sub-megabase domains (TADs). It remains unclear, however, how these layers of organization form, interact with one another and influence genome function. Here we show that deletion of the cohesin-loading factor Nipbl in mouse liver leads to a marked reorganization of chromosomal folding. TADs and associated Hi-C peaks vanish globally, even in the absence of transcriptional changes...
November 2, 2017: Nature
https://www.readbyqxmd.com/read/29093029/chromatin-conformation-links-distal-target-genes-to-ckd-loci
#10
Maarten M Brandt, Claartje A Meddens, Laura Louzao-Martinez, Noortje A M van den Dungen, Nico R Lansu, Edward E S Nieuwenhuis, Dirk J Duncker, Marianne C Verhaar, Jaap A Joles, Michal Mokry, Caroline Cheng
Genome-wide association studies (GWASs) have identified many genetic risk factors for CKD. However, linking common variants to genes that are causal for CKD etiology remains challenging. By adapting self-transcribing active regulatory region sequencing, we evaluated the effect of genetic variation on DNA regulatory elements (DREs). Variants in linkage with the CKD-associated single-nucleotide polymorphism rs11959928 were shown to affect DRE function, illustrating that genes regulated by DREs colocalizing with CKD-associated variation can be dysregulated and therefore, considered as CKD candidate genes...
November 1, 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/29091999/evaluation-and-comparison-of-methods-for-recapitulation-of-3d-spatial-chromatin-structures
#11
Jincheol Park, Shili Lin
How chromosomes fold and how distal genomic elements interact with one another at a genomic scale have been actively pursued in the past decade following the seminal work describing the Chromosome Conformation Capture (3C) assay. Essentially, 3C-based technologies produce two-dimensional (2D) contact maps that capture interactions between genomic fragments. Accordingly, a plethora of analytical methods have been proposed to take a 2D contact map as input to recapitulate the underlying whole genome three-dimensional (3D) structure of the chromatin...
October 30, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/29080874/-computer-methods-of-analysis-of-chromosome-contacts-in-the-cell-nucleus-based-on-sequencing-technology-data
#12
Y L Orlov, O Thierry, A G Bogomolov, A V Tsukanov, E V Kulakova, E R Galieva, A O Bragin, G Li
The study spatial chromosome structure and chromosome folding in the interphase cell nucleus is an important challenge of world science. Detection of eukaryotic genome regions that physically interact with each other could be done by modern sequencing technologies. A basic method of chromosome folding by total sequencing of contacting DNA fragments is HI-C. Long-range chromosomal interactions play an important role in gene transcription and regulation. The study of chromosome interactions, 3D (three-dimensional) genome structure and its effect on gene transcription allows revealing fundamental biological processes from a viewpoint of structural regulation and are important for cancer research...
October 2017: Biomedit︠s︡inskai︠a︡ Khimii︠a︡
https://www.readbyqxmd.com/read/29074623/conformational-dynamics-of-the-ttd-phd-histone-reader-module-of-uhrf1-reveals-multiple-histone-binding-states-allosteric-regulation-and-druggability
#13
R Scott Houliston, Alexander Lemak, Aman Iqbal, Danton Ivanochko, Shili Duan, Lilia Kaustov, Michelle S Ong, Lixin Fan, Guillermo Senisterra, Peter J Brown, Yun-Xing Wang, Cheryl H Arrowsmith
UHRF1 is a key mediator of inheritance of epigenetic DNA methylation patterns during cell division and is a putative target for cancer therapy. Recent studies indicate that interdomain interactions critically influence UHRF1's chromatin-binding properties, including allosteric regulation of its histone binding. Here, using an integrative approach that combines small angle X-ray scattering (SAXS), NMR spectroscopy, and molecular dynamics (MD) simulations, we characterized the dynamics of the TTD-PHD histone reader module, including its 20-residue interdomain linker...
October 26, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29065928/chromatin-status-and-transcription-factor-binding-to-gonadotropin-promoters-in-gonadotrope-cell-lines
#14
Huimin Xie, Hanne M Hoffmann, Anita K Iyer, Melissa J Brayman, Cindy Ngo, Mary Jean Sunshine, Pamela L Mellon
BACKGROUND: Proper expression of key reproductive hormones from gonadotrope cells of the pituitary is required for pubertal onset and reproduction. To further our understanding of the molecular events taking place during embryonic development, leading to expression of the glycoproteins luteinizing hormone (LH) and follicle-stimulating hormone (FSH), we characterized chromatin structure changes, imparted mainly by histone modifications, in model gonadotrope cell lines. METHODS: We evaluated chromatin status and gene expression profiles by chromatin immunoprecipitation assays, DNase sensitivity assay, and RNA sequencing in three developmentally staged gonadotrope cell lines, αT1-1 (progenitor, expressing Cga), αT3-1 (immature, expressing Cga and Gnrhr), and LβT2 (mature, expressing Cga, Gnrhr, Lhb, and Fshb), to assess changes in chromatin status and transcription factor access of gonadotrope-specific genes...
October 24, 2017: Reproductive Biology and Endocrinology: RB&E
https://www.readbyqxmd.com/read/29058599/evidence-of-reduced-recombination-rate-in-human-regulatory-domains
#15
Yaping Liu, Abhishek Sarkar, Pouya Kheradpour, Jason Ernst, Manolis Kellis
BACKGROUND: Recombination rate is non-uniformly distributed across the human genome. The variation of recombination rate at both fine and large scales cannot be fully explained by DNA sequences alone. Epigenetic factors, particularly DNA methylation, have recently been proposed to influence the variation in recombination rate. RESULTS: We study the relationship between recombination rate and gene regulatory domains, defined by a gene and its linked control elements...
October 20, 2017: Genome Biology
https://www.readbyqxmd.com/read/29057826/potential-role-of-phase-separation-of-repetitive-dna-in-chromosomal-organization
#16
Shao-Jun Tang
The basic principles of chromosomal organization in eukaryotic cells remain elusive. Current mainstream research efforts largely concentrate on searching for critical packaging proteins involved in organizing chromosomes. I have taken a different perspective, by considering the role of genomic information in chromatins. In particular, I put forward the concept that repetitive DNA elements are key chromosomal packaging modules, and their intrinsic property of homology-based interaction can drive chromatin folding...
October 18, 2017: Genes
https://www.readbyqxmd.com/read/29053968/multiscale-3d-genome-rewiring-during-mouse-neural-development
#17
Boyan Bonev, Netta Mendelson Cohen, Quentin Szabo, Lauriane Fritsch, Giorgio L Papadopoulos, Yaniv Lubling, Xiaole Xu, Xiaodan Lv, Jean-Philippe Hugnot, Amos Tanay, Giacomo Cavalli
Chromosome conformation capture technologies have revealed important insights into genome folding. Yet, how spatial genome architecture is related to gene expression and cell fate remains unclear. We comprehensively mapped 3D chromatin organization during mouse neural differentiation in vitro and in vivo, generating the highest-resolution Hi-C maps available to date. We found that transcription is correlated with chromatin insulation and long-range interactions, but dCas9-mediated activation is insufficient for creating TAD boundaries de novo...
October 19, 2017: Cell
https://www.readbyqxmd.com/read/29052195/technical-review-a-hitchhiker-s-guide-to-chromosome-conformation-capture
#18
Stefan Grob, Giacomo Cavalli
The introduction of chromosome conformation capture (3C) technologies boosted the field of 3D-genome research and significantly enhanced the available toolset to study chromosomal architecture. 3C technologies not only offer increased resolution compared to the previously dominant cytological approaches but also allow the simultaneous study of genome-wide 3D chromatin contacts, thereby enabling a candidate-free perspective on 3D-genome architecture. Since its introduction in 2002, 3C technologies evolved rapidly and now constitute a collection of tools, each with their strengths and pitfalls with respect to specific research questions...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29048467/identification-of-copy-number-variations-and-translocations-in-cancer-cells-from-hi-c-data
#19
Abhijit Chakraborty, Ferhat Ay
Motivation: Eukaryotic chromosomes adapt a complex and highly dynamic three-dimensional (3D) structure, which profoundly affects different cellular functions and outcomes including changes in epigenetic landscape and in gene expression. Making the scenario even more complex, cancer cells harbor chromosomal abnormalities (e.g., copy number variations (CNVs) and translocations) altering their genomes both at the sequence level and at the level of 3D organization. High-throughput chromosome conformation capture techniques (e...
October 18, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29044247/regulation-of-genome-organization-and-gene-expression-by-nuclear-mechanotransduction
#20
REVIEW
Caroline Uhler, G V Shivashankar
It is well established that cells sense chemical signals from their local microenvironment and transduce them to the nucleus to regulate gene expression programmes. Although a number of experiments have shown that mechanical cues can also modulate gene expression, the underlying mechanisms are far from clear. Nevertheless, we are now beginning to understand how mechanical cues are transduced to the nucleus and how they influence nuclear mechanics, genome organization and transcription. In particular, recent progress in super-resolution imaging, in genome-wide application of RNA sequencing, chromatin immunoprecipitation and chromosome conformation capture and in theoretical modelling of 3D genome organization enables the exploration of the relationship between cell mechanics, 3D chromatin configurations and transcription, thereby shedding new light on how mechanical forces regulate gene expression...
October 18, 2017: Nature Reviews. Molecular Cell Biology
keyword
keyword
53537
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"